Digital Commons Network^™

Increasing Statistical Literacy By Exploiting Lexical Ambiguity Of Technical Terms, Jennifer J. Kaplan, Neal Rogness

Numeracy

Instructional inattention to language poses a barrier for students in entry-level science courses, in part because students may perceive a subject as difficult solely based on the lack of understanding of the vocabulary. In addition, the technical use of terms that have different everyday meanings may cause students to misinterpret statements made by instructors, leading to an incomplete or incorrect understanding of the domain. Terms that have different technical and everyday meanings are said to have lexical ambiguity and statistics, as a discipline, has many lexically ambiguous terms. This paper presents a cyclic process for designing activities to address lexical …

Small Genome Separates Native And Invasive Populations In An Ecologically Important Cosmopolitan Grass, Petr Pyšek, Hana Skálová, Jan Čuda, Wen-Yong Guo, Jan Suda, Jan Doležal, Ondřej Kauzál, Carla Lambertini, Magdalena Lučanová, Terezie Mandáková, Lenka Moravcová, Klára Pyšková, Hans Brix, Laura A. Meyerson

Natural Resources Science Faculty Publications

The literature suggests that small genomes promote invasion in plants, but little is known about the interaction of genome size with other traits or about the role of genome size during different phases of the invasion process. By intercontinental comparison of native and invasive populations of the common reed Phragmites australis, we revealed a distinct relationship between genome size and invasiveness at the intraspecific level. Monoploid genome size was the only significant variable that clearly separated the North American native plants from those of European origin. The mean Cx value (the amount of DNA in one chromosome set) for …

Ontogenetic Partial Migration Is Associated With Environmental Drivers And Influences Fisheries Interactions In A Marine Predator, James S E Lea, Bradley M. Wetherbee, Lara L. Sousa, Choy Aming, Neil Burnie, Nicholas E. Humphries, Nuno Queiroz, Guy M. Harvey, David W. Sims, Mahmood S. Shivji

Biological Sciences Faculty Publications

The ability to predict animal movement based on environmental change is essential for understanding the dynamic nature of their spatial ecology, and in turn the effectiveness of conservation strategies. We used a large marine predator that displays partial migration (the tiger shark Galeocerdo cuvier) as a model to test the role of oceanic conditions in predicting the space-use of different size classes. By using generalized additive mixed models (GAMMs), we revealed that environmental variables (sea surface temperature, primary productivity, thermal fronts, and bathymetry) had much greater predictive power for the movements of large, migratory tiger sharks than for small, …

Consensus Coding Sequence (Ccds) Database: A Standardized Set Of Human And Mouse Protein-Coding Regions Supported By Expert Curation., Shashikant Pujar, Nuala A O'Leary, Catherine M Farrell, Jane E Loveland, Jonathan M Mudge, Craig Wallin, Carlos G Girón, Mark Diekhans, If Barnes, Ruth Bennett, Andrew E Berry, Eric Cox, Claire Davidson, Tamara Goldfarb, Jose M Gonzalez, Toby Hunt, John Jackson, Vinita Joardar, Mike P Kay, Vamsi K Kodali, Fergal J Martin, Monica Mcandrews, Kelly M Mcgarvey, Michael Murphy, Bhanu Rajput, Sanjida H Rangwala, Lillian D Riddick, Ruth L Seal, Marie-Marthe Suner, David Webb, Sophia Zhu, Bronwen L Aken, Elspeth A Bruford, Carol J Bult, Adam Frankish, Terence Murphy, Kim D Pruitt

Faculty Research 2018

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration …

Tumorfusions: An Integrative Resource For Cancer-Associated Transcript Fusions., Xin Hu, Qianghu Wang, Ming Tang, Floris P Barthel, Samirkumar B Amin, Kosuke Yoshihara, Frederick M Lang, Emmanuel Martinez-Ledesma, Soo Hyun Lee, Siyuan Zheng, Roel G W Verhaak

Faculty Research 2018

Gene fusion represents a class of molecular aberrations in cancer and has been exploited for therapeutic purposes. In this paper we describe TumorFusions, a data portal that catalogues 20 731 gene fusions detected in 9966 well characterized cancer samples and 648 normal specimens from The Cancer Genome Atlas (TCGA). The portal spans 33 cancer types in TCGA. Fusion transcripts were identified via a uniform pipeline, including filtering against a list of 3838 transcript fusions detected in a panel of 648 non-neoplastic samples. Fusions were mapped to somatic DNA rearrangements identified using whole genome sequencing data from 561 cancer samples as …

Metavirome Sequencing Of The Termite Gut Reveals The Presence Of An Unexplored Bacteriophage Community, Chinmay V. Tikhe, Claudia Husseneder

Faculty Publications

The Formosan subterranean termite; Coptotermes formosanus is nutritionally dependent on the complex and diverse community of bacteria and protozoa in their gut. Although, there have been many studies to decipher the taxonomic and functional diversity of bacterial communities in the guts of termites, their bacteriophages remain unstudied. We sequenced the metavirome of the guts of Formosan subterranean termite workers to study the diversity of bacteriophages and other associated viruses. Results showed that the termites harbor a virome in their gut comprised of varied and previously unknown bacteriophages. Between 87-90% of the predicted dsDNA virus genes by Metavir showed similarity to …

Component Tree Analysis Of Cystovirus Φ6 Nucleocapsid Cryo-Em Single Particle Reconstructions, Lucas Oliveira, Ze Ye, Al Katz, Alexandra Alimova, Hui Wei, Gabor T. Herman, Paul Gottlieb

Publications and Research

The 3-dimensional structure of the nucleocapsid (NC) of bacteriophage φ6 is described utilizing component tree analysis, a topological and geometric image descriptor. The component trees are derived from density maps of cryo-electron microscopy single particle reconstructions. Analysis determines position and occupancy of structure elements responsible for RNA packaging and transcription. Occupancy of the hexameric nucleotide triphosphorylase (P4) and RNA polymerase (P2) are found to be essentially complete in the NC. The P8 protein lattice likely fixes P4 and P2 in place during maturation. We propose that the viral procapsid (PC) is a dynamic structural intermediate where the P4 and P2 …

Exosomes Serve As Novel Modes Of Tick-Borne Flavivirus Transmission From Arthropod To Human Cells And Facilitates Dissemination Of Viral Rna And Proteins To The Vertebrate Neuronal Cells, Wenshuo Zhou, Michael Woodson, Biswas Neupane, Fengwei Bai, Michael B. Sherman, Kyung H. Choi, Girish Neelakanta, Hameeda Sultana

Faculty Publications

Molecular determinants and mechanisms of arthropod-borne flavivirus transmission to the vertebrate host are poorly understood. In this study, we show for the first time that a cell line from medically important arthropods, such as ticks, secretes extracellular vesicles (EVs) including exosomes that mediate transmission of flavivirus RNA and proteins to the human cells. Our study shows that tick-borne Langat virus (LGTV), a model pathogen closely related to tick-borne encephalitis virus (TBEV), profusely uses arthropod exosomes for transmission of viral RNA and proteins to the human- skin keratinocytes and blood endothelial cells. Cryo-electron microscopy showed the presence of purified arthropod/neuronal exosomes …

Geochemical Characteristics Of Soils On Ellis Island, New York-New Jersey, Sixty Years After The Abandonment Of The Hospital Complex, Kaixuan Bu, Deborah Freile, James Cizdziel, Jena Richards, Virinder Sidhu, Nurdan Duzgoren-Aydin

Faculty and Student Publications (Open Access)

Soil plays many critical roles in ecosystem health. As urbanization expands into once industrial and commercial lands, there is increased potential for human exposure to soil contaminants, including heavy metals introduced by past anthropogenic activities. Thus, it is important to assess soil contamination in such areas for public health concerns. In this study, we investigated the physico-chemical characteristics of soils from an abandoned hospital complex on Ellis Island, New York (NY) – New Jersey (NJ) to assess the geochemical conditions of the local soil environment and metal contamination from historical activities, including coal-burning and use of lead arsenate insecticide and …

Dietary Supplements: Regulatory Challenges And Research Resources, Johanna Dwyer, Paul Coates, Michael Smith

Faculty and Student Publications (Open Access)

Many of the scientific and regulatory challenges that exist in research on the safety, quality and efficacy of dietary supplements are common to all countries as the marketplace for them becomes increasingly global. This article summarizes some of the challenges in supplement science and provides a case study of research at the Office of Dietary Supplements at the National Institutes of Health, USA, along with some resources it has developed that are available to all scientists. It includes examples of some of the regulatory challenges faced and some resources for those who wish to learn more about them.

An Intracellular Activation Of Smoothened That Is Independent Of Hedgehog Stimulation In Drosophila, Kai Jiang, Yajuan Liu, Jie Zhang, Jianhang Jia

Markey Cancer Center Faculty Publications

Smoothened (Smo), a GPCR family protein, plays a critical role in the reception and transduction of Hedgehog (Hh) signal. Smo is phosphorylated and activated on the cell surface; however, it is unknown whether Smo can be intracellularly activated. Here, we demonstrate that inactivation of the ESCRT-III causes dramatic accumulation of Smo in the ESCRT-III/MVB compartment, and subsequent activation of Hh signaling. In contrast, inactivation of ESCRTs 0–II induces mild Smo accumulation in the ESCRT-III/MVB compartment. We provide evidence that Kurtz (Krz), the Drosophila β-arrestin2, acts in parallel with the ESCRTs 0-II pathway to sort Smo to the multivesicular bodies and …

Stemmapper: A Curated Gene Expression Database For Stem Cell Lineage Analysis, Jose P. Pinto, Rsr Machado, Ramiro Magno, Daniel V. Oliveira, S Machado, Raquel P. Andrade, J Bragança, Isabel Duarte, Matthias E. Futschik

School of Biomedical Sciences

No abstract provided.

Demonstration Of Translation Elongation Factor 3 Activity From A Non-Fungal Species, Phytophthora Infestans, Maria K. Mateyak, Justyna K. Pupek, Alexandra E. Garino, Mccllelan C. Knapp, Sarah F. Colmer, Terri Goss Kinzy, Stephen Dunaway

Faculty Publications – Biological Sciences

In most eukaryotic organisms, translation elongation requires two highly conserved elongation factors eEF1A and eEF2. Fungal systems are unique in requiring a third factor, the eukaryotic Elongation Factor 3 (eEF3). For decades, eEF3, a ribosome-dependent ATPase, was considered “fungal-specific”, however, recent bioinformatics analysis indicates it may be more widely distributed among other unicellular eukaryotes. In order to determine whether divergent eEF3-like proteins from other eukaryotic organisms can provide the essential functions of eEF3 in budding yeast, the eEF3-like proteins from Schizosaccharomyes pombe and an oomycete, Phytophthora infestans, were cloned and expressed in Saccharomyces cerevisiae. Plasmid shuffling experiments showed …

Childhood Interrupted: An Autoethnography Of Supporting Learning, Development, And Foster Parenting, Alica Legaye Benton

LSU Doctoral Dissertations

The purpose of this autoethnography is to investigate my adopted child’s literacy skills and the impact an interrupted childhood has on literacy development. Learning to read and write encompasses multiple facets of cognition and aspiration. An autoethnography of multiple interruptions in this child’s formative years while fostering her literacy development will be chronicled, examined, analyzed, and interpreted. This autoethnography focuses on the acquisition of oral language and early reading and writing skills when there is a loss of childhood stability. Data were collected through observations, artifacts, and a reflective journal. Data were analyzed using eclectic coding in order to identify …

We Are...Marshall, January 3, 2018, Office Of Marshall University Communications

We Are ... Marshall: the Newsletter for Marshall University 1999-2023

No abstract provided.

16s And Coi Barcoding Sequences For Crustaceans Collected From The Northern Gulf Of Mexico For Cruises Dp02, Dp03, And Dp04 From August 2015 - August 2016, Heather Bracken-Grissom Dr.

DEEPEND Datasets

These are the 16S and COI barcoding sequences for crustaceans collected on cruises DP02, DP03, and DP04. These barcodes, obtained from the species we collected, will be used to aid in species identification efforts, evolutionary relationships analyses, adult-larval linkages, and new species discoveries. Samples were taken from animals collected during cruises that took place in the northern Gulf of Mexico from August 2015 - August 2016.

Environmental Influence On Petroleum Products Quality, Sh.B. Urinbaeva, М.М. Tashpulatov, R. Sayfutdinov

Acta of Turin Polytechnic University in Tashkent

In the article is considered the regularities of microbiological damage of fuel - lubricants.

Increased Fluxes Of Shelf-Derived Materials To The Central Arctic Ocean, Lauren Kipp, Matthew A. Charette, Willard S. Moore, Paul B. Henderson, Ignatius G. Rigor

School of Earth & Environment Departmental Research

Rising temperatures in the Arctic Ocean region are responsible for changes such as reduced ice cover, permafrost thawing, and increased river discharge, which, together, alter nutrient and carbon cycles over the vast Arctic continental shelf. We show that the concentration of radium-228, sourced to seawater through sediment-water exchange processes, has increased substantially in surface waters of the central Arctic Ocean over the past decade. A mass balance model for 228Ra suggests that this increase is due to an intensification of shelf-derived material inputs to the central basin, a source that would also carry elevated concentrations of dissolved organic carbon and …

Biology's Foster Featured In Ohio Magazines Excellence In Education Issue, Ohio University College Of Arts & Sciences

All Forum Articles

No abstract provided.

Electron Effective Mass In Sn-Doped Monoclinic Single Crystal B-Gallium Oxide Determined By Mid-Infrared Optical Hall Effect, Sean Knight, Alyssa Mock, Rafal Korlacki, Vanya Darakchieva, Bo Monemar, Yoshinao Kumagai, Ken Goto, Masataka Higashiwaki, Mathias Schubert

Department of Electrical and Computer Engineering: Faculty Publications

The isotropic average conduction band minimum electron effective mass in Sn-doped monoclinic single crystal B-Ga₂O₃ is experimentally determined by the mid-infrared optical Hall effect to be (0.28460.013)m₀ combining investigations on (010) and (_201) surface cuts. This result falls within the broad range of values predicted by theoretical calculations for undoped B-Ga₂O₃. The result is also comparable to recent density functional calculations using the Gaussian-attenuation- Perdew-Burke-Ernzerhof hybrid density functional, which predict an average effective mass of 0.267m₀. Within our uncertainty limits, we detect no anisotropy for the electron effective mass, which …

Cuteness And Appeals: Unleashing Prosocial Emotions, Katherine (Kivy) Weeks

Doctoral Dissertations

The purpose of this dissertation is to explore the implications of cuteness in marketing communication. It uses babyfacedness research as the basis for evoking a cuteness response, and introduces a nurturance scale to measure the emotional outcome of exposure. In the process, it uncovered problems with existing conceptualizations of attractiveness, and demonstrated how using nurturance, aesthetic judgement and sexual judgement measures better explains aggregate emotional outcome (e.g. positive/negative emotion) from exposure to facial images. In particular, it shows how nurturance and sexual judgements have antagonistic effects on aggregate emotion. Additionally, it details how babyfaced manipulations influence both the perceived age …

Better Than Before, Makia Harper

Theses and Dissertations

Better than Before is an experiential art installation that profiles the life of James Isreal, a Vietnam vet who shares a spiritual journey that is filled with self-discovery, introspection, and hope in the midst of war and abhorrent racism. His poignant retrospective follows his struggle to find peace in the midst of trauma and disease, providing life lessons that transcend the pangs of adversity and the unknown.

Analysis Of Veterinary Drug Residues In Imported And Domestic Crawfish Using Liquid Chromatography—Mass Spectrometry, Emily Kate Wall

LSU Master's Theses

Aquaculture production has greatly increased over the past few decades, and will continue to grow as the world fisheries become overfished and demand for seafood increases. With increased production comes more intense cultivation methods and heavy use of formulated feeds that may contain veterinary drug residues. Currently no antibiotics are allowed in the U.S. for crawfish aquaculture; yet, detectable levels of various antibiotics have been found in imported seafood samples.The FDA is responsible for testing aquaculture products entering the United States, but only has the capabilities to test a minimal amount of those imports. Additionally, for crawfish there is only …

Sooty Mangabey Genome Sequence Provides Insight Into Aids Resistance In A Natural Siv Host, David Palesch, Steven E. Bosinger, Gregory K. Tharp, Thomas H. Vanderford, Mirko Paiardini, Ann Chahroudi, Zachary P. Johnson, Frank Kirchhoff, Beatrice H. Hahn, Robert B. Norgren, Nirav B. Patel, Donald L. Sodora, Reem A. Dawoud, Caro-Beth Stewart, Sara M. Seepo, R. Alan Harris, Yue Liu, Muthuswamy Raveendran, Yi Han, Adam English, Gregg W.C. Thomas, Matthew W. Hahn, Lenore Pipes, Christopher E. Mason, Donna M. Muzny, Richard A. Gibbs, Daniel Sauter, Kim Worley, Jeffrey Rogers, Guido Silvestri

Journal Articles: Genetics, Cell Biology & Anatomy

In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodeficiency virus (SIV) in macaques, SIV infection of a natural host, sooty mangabeys (Cercocebus atys), is non-pathogenic despite high viraemia. Here we sequenced and assembled the genome of a captive sooty mangabey. We conducted genome-wide comparative analyses of transcript assemblies from C. atys and AIDS-susceptible species, such as humans and macaques, to identify candidates for host genetic factors that influence susceptibility. We identified several immune-related genes in the genome of C. atys that show substantial sequence divergence from macaques or humans. One of these sequence divergences, a …

Comparison Of African And North American Velvet Ant Mimicry Complexes: Another Example Of Africa As The 'Odd Man Out', Joseph S. Wilson, Aaron D. Pan, Erica S. Limb, Kevin A. Williams

Biology Faculty Publications

Africa has the most tropical and subtropical land of any continent, yet has relatively low species richness in several taxa. This depauperate nature of the African tropical fauna and flora has led some to call Africa the “odd man out.” One exception to this pattern is velvet ants (Hymenoptera: Mutillidae), wingless wasps that are known for Müllerian mimicry. While North American velvet ants form one of the world’s largest mimicry complexes, mimicry in African species has not been investigated. Here we ask do African velvet ant Müllerian mimicry rings exist, and how do they compare to the North American complex. …

Temozolomide, Sirolimus And Chloroquine Is A New Therapeutic Combination That Synergizes To Disrupt Lysosomal Function And Cholesterol Homeostasis In Gbm Cells, Minesh Mehta

All Publications

Glioblastoma (GBM) cells are characterized by high phagocytosis, lipogenesis, exocytosis activities, low autophagy capacity and high lysosomal demand are necessary for survival and invasion. The lysosome stands at the cross roads of lipid biosynthesis, transporting, sorting between exogenous and endogenous cholesterol. We hypothesized that three already approved drugs, the autophagy inducer, sirolimus (rapamycin, Rapa), the autophagy inhibitor, chloroquine (CQ), and DNA alkylating chemotherapy, temozolomide (TMZ) could synergize against GBM. This repurposed triple therapy combination induced GBM apoptosis in vitro and inhibited GBM xenograft growth in vivo. Cytotoxicity is caused by induction of lysosomal membrane permeabilization and release of hydrolases, …

Investigation Into Reynolds Number Effects On A Biomimetic Flapping Wing, Daniel K. Hope, Anthony M. Deluca, Ryan P. O'Hara

Faculty Publications

This research investigated the behavior of a Manduca sexta inspired biomimetic wing as a function of Reynolds number by measuring the aerodynamic forces produced by varying the characteristic wing length and testing at air densities from atmospheric to near vacuum. A six degree of freedom balance was used to measure forces and moments, while high speed cameras were used to measure wing stroke angle. An in-house created graphical user interface was used to vary the voltage of the drive signal sent to the piezoelectric actuator which determined the wing stroke angle. The Air Force Institute of Technology baseline 50 mm …

Disparities In Breast Cancer Stage At Diagnosis: Importance Of Race, Poverty, And Age, Faustine Williams, Emmanuel Thompson

Journal of Health Disparities Research and Practice

This study investigated the association of race, age, and census tract area poverty level on breast cancer stage at diagnosis. The study was limited to women residing in Missouri, aged 18 years and older, diagnosed with breast cancer, and whose cases were reported to the Cancer Registry between 2003 and 2008. The risk, relative risk, and increased risk of late-stage at diagnosis by race, age, and census tract area poverty level were computed. We found that the odds of late-stage breast cancer among African-American women were higher when compared with their white counterpart (OR 1.433; 95% CI, 1.316, 1.560). In …

Demographics And Cardiovascular Risk Factors In A Bi-Ethnic Church-Based Intervention: Baseline Results Of The Stroke Health And Risk Education (Share) Project, Lesli Skolarus

Journal of Health Disparities Research and Practice

Objectives: Hispanics have a higher incidence of cardiovascular disease (CVD) than non-Hispanic whites (NHWs). Despite proven benefits in other minority populations, few interventions have been conducted in partnership with Churches with substantial Hispanic membership. In this context, we describe the baseline demographics and CVD risk factors among participants of a bi-ethnic Catholic Church-based CVD prevention trial.

Methods: The Stroke Health and Risk Education (SHARE) project was a cluster-randomized, multi-component, faith-based, behavioral intervention that enrolled Mexican Americans (MAs) and NHWs from Catholic Churches in Corpus Christi, Texas. Strategies to ensure MA recruitment included bilingual staff and materials and partnership with Catholic …

Henry Rosemont, Jr: Logician And Lotus-Eater, Ronnie Littlejohn

Comparative Philosophy

No abstract provided.